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Forensic Characterization of 15 Autosomal Strs in Four Populations

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Forensic Characterization of 15 Autosomal Strs in Four Populations www.nature.com/scientificreports OPEN Forensic characterization of 15 autosomal STRs in four populations from Xinjiang, China, and genetic Received: 15 December 2017 Accepted: 5 March 2018 relationships with neighboring Published: xx xx xxxx populations Xiaoni Zhan1, Atif Adnan 1, Yuzhang Zhou1, Amjad Khan1, Kadirya Kasim1 & Dennis McNevin2 The Xinjiang Uyghur Autonomous Region of China (XUARC) harbors 47 ethnic groups including the Manchu (MCH: 0.11%), Mongols (MGL: 0.81%), Kyrgyz (KGZ: 0.86%) and Uzbek (UZK: 0.066%). To establish DNA databases for these populations, allele frequency distributions for 15 autosomal short tandem repeat (STR) loci were determined using the AmpFlSTR Identifler PCR amplifcation kit. There was no evidence of departures from Hardy–Weinberg equilibrium (HWE) in any of the four populations and minimal departure from linkage equilibrium (LE) for a very small number of pairwise combinations of loci. The probabilities of identity for the diferent populations ranged from 1 in 1.51 × 1017 (MCH) to 1 in 9.94 × 1018 (MGL), the combined powers of discrimination ranged from 0.99999999999999999824 (UZK) to 0.9999999999999999848 (MCH) and the combined probabilities of paternal exclusion ranged from 0.9999979323 (UZK) to 0.9999994839 (MCH). Genetic distances, a phylogenetic tree and principal component analysis (PCA) revealed that the MCH, KGZ and UZK are genetically closer to the Han population of Liaoning and the Mongol population of Mongolia while the MGL are closer to Han, Japanese, Korean, Malaysian, Hong Kong Han and Russians living in China. Xinjiang is a multi-ethnic region and has played an important role in connecting eastern Eurasia and western Eurasia. It was crossed by the famous Silk Road, which linked trade between East Asia, Central Asia, and Europe1. Many ethnic groups, including the Manchu (MCH), Mongols (MGL), Kirgiz (KGZ) and Uzbek (UZK) have lived there for hundreds of years2. Te Manchu founded two Chinese Dynasties on the country’s inner plains: the Jin Dynasty, founded by the Nvzhen people, and the Qing Dynasty, founded by Huang Taijin in 1635. Te history of the Manchu can be traced back 6000–7000 years ago (6–7 kya). Although the Manchu people can be found in all over China3, they represent only 0.11% of the Xinjiang population4. Te Mongols came from the area around the east bank of the ancient Wangjian River (present-day Eerguna River) in Inner Mongolia. “Mengwu” is the earliest Chinese name for “Mongolia”. It frst appeared in the Tang dynasty (618–907). “Mongol” was initially the name for one of the Mongolian tribes. At the beginning of the 13th century, the Mongolian tribe headed by Genghis Khan unifed the other tribes in the region and gradually formed a new ethnic community. Terefore, “Mongolia” became the name for a nationality instead of a tribe5. As well as Mongolia, Mongols currently live mainly in the Inner Mongolia Autonomous Region and some prefectures of Xinjiang Uygur Autonomous Region like Bayingolin (South East) and Bortala (North West). Tey represent 0.81% of the Xinjiang population4. Te Kyrgyz (or Kirgiz) live mainly in the southwest of Xinjiang, especially in the Kezhilesu Kyrgyz autono- mous state. Tey have a long history and have been known in China by many names. In the Han dynasty, they were called “Gekun” or “Jiankun”. Later they were called “Qigu” in the Jin dynasty; “Jiankun”, “Jikasi” or “Qiliqisi” 1Department of Forensic Genetics, School of Forensic Medicine, China Medical University, Shenyang, 110122, P.R. China. 2National Centre for Forensic Studies, Faculty of Science & Technology, University of Canberra, Canberra, Australia. Xiaoni Zhan and Atif Adnan contributed equally to this work. Correspondence and requests for materials should be addressed to A.A. (email: [email protected]) SCIENTIFIC REPORTS | (2018) 8:4673 | DOI:10.1038/s41598-018-22975-6 1 www.nature.com/scientificreports/ in the Tang and Song dynasty; and “Jirjisi” or “Qirjisi” in the Yuan and Ming periods. All these names were based on “Kyrgyz”, which has had diferent Chinese translation at diferent times. Te etymology of “Kyrgyz” is thought to be “40 tribes” or “40 girls”2. While the Kyrgyz are primarily located in Kyrgyzstan, they represent only 0.86% of the Xinjiang population4. Te name “Uzbek” frst originated with Uzbek Khan, a local ruler in the Mongol Empire in the 14th century. Te Uzbeks are an ancient Iranian people that intermingled with nomadic Mongol and Turkic tribes that invaded Central Asia between the 11th and 15th centuries. Te Uzbeks that live in China live mostly in Xinjiang near the border with Russia and the former Soviet Central Asian republics. Uzbeks have been trading in western China for centuries. In the 16th century, they began to settle in cities in Xinjiang. Most Uzbeks in China still live in the cities and are engaged in trading or business1. Tey represent 0.066% of the Xinjiang population4. Short tandem repeat (STR) loci, also referred to as microsatellites or simple sequence repeats (SSRs), are DNA sequences that contain a repeat motif of 2–6 bp and are characterized by a high level of relatively stable polymorphisms, a dense, uniform chromosomal distribution as well as short sequence lengths, which facilitates detection and analysis by PCR and sequencing6,7. All these features render STRs as powerful genetic markers for inter-population studies8 and for the reconstruction of recent human evolutionary history9. In view of their high level of variability, autosomal STRs have been the most common genetic markers used in forensic applications, including personal identifcation and paternity testing10. Most forensic laboratories use commercially available kits for multiple STR genotyping11. Tere have been previous studies of STR genotypes in the Uighur12 and Kazak13 populations of Xinjiang but the Manchu, Mongol, Kyrgyz and Uzbek populations remain uncharacterised. In the present study, the 15auto- somal STRs in the AmpFLSTR Identifler kit (Applied Biosystems, Foster City, CA, USA) were examined in the MCH, MGL, KGZ and UZK minorities of the Xinjiang Uyghur Autonomous Region (XUAR). Results and Discussion Forensic parameters. Te distribution of allele frequencies and forensic statistical parameters in the four Xinjiang ethnic minorities are available as Supplementary Data (Supplementary Tables 1, 2, 3 and 4). Totals of 152, 165, 153 and 168 unique alleles were found in the Manchu, Mongol, Kyrgyz and Uzbek populations, respectively. Te combined powers of discrimination (CPDs) for the 15 STR loci were 0.999 999 999 999 999 984 833, 0.999 999 999 999 999 990 057, 0.999 999 999 999 999 996 333 and 0.999 999 999 999 999 998 244, respectively. Te combined powers of exclusion (CPE) for the 15 STR loci were 0.999 999 416, 0.999 999 483, 0.999 997 932 and 0.999 998 973, respectively. Te probabilities of identity for the diferent populations were 1/1.51 × 1017, 1/1.75 × 1018, 1/3.66 × 1018 and to 1/9.94 × 1018, respectively. D2S1338 had the highest heterozy- gosities and powers of discrimination (PDs) in all four populations. FGA was the most polymorphic locus in the Mongol (20 unique alleles) and Uzbek (19 unique alleles) populations, respectively. D18S51 was most poly- morphic in the Manchu population (18 unique alleles) while D18S51, D21S11 and FGA all had 15 unique alleles in the Kyrgyz population. Informativeness can be quantitatively measured by the polymorphism information content. Teoretically, PIC values can range from 0 to 1. At a PIC of 0, the marker has only one allele. At a PIC of 1, the marker would have an infnite number of alleles. A PIC value of greater than 0.7 is considered to be highly informative. Clearly, markers with greater numbers of alleles tend to have higher PIC values and thus are more informative14. Te Manchu and Mongol populations have four loci with PIC < 0.7 while the Uzbek and Kyrgyz populations have only two loci with PIC < 0.7. Terefore, most loci exhibited a high informativeness, showing the potential of the Identifler panel for diferentiation of individuals and for paternity testing for the four ethnic minority populations in the Xinjiang Uyghur Autonomous Region of China. Hardy-Weinberg equilibrium (HWE). All of the loci were in Hardy-Weinberg Equilibrium (HWE) in the Kyrgyz population (p > 0.05), while one STR locus was out of HWE for Manchu (D7S820), two loci for Mongol (CSF1PO, D19S433) and four loci for Uzbek (D18S51, D2S1338, D7S820 and FGA). However, when a sequential Bonferroni correction15 was applied to mitigate against the so-called “multiple comparison problem” (where for a signifcant p-value of 0.5, 5% of tests are likely to be signifcant by chance), no loci in any of the four populations were found to be out of HWE (Supplementary Table 5). Linkage equilibrium (LE). Linkage disequilibrium (LD) can be caused by association between adjacent alleles co-inherited from single, ancestral chromosomes but may also be a result of selection, random genetic drif, the rate of mutation or recombination, nonrandom mating, founder efects, sampling efects, recent admix- ture, and population substructure16. Exact tests for linkage equilibrium (LE) showed that the p-values of 50 pair- wise combinations of STR loci (11 in Mongolia and Manchu, 13 in Kyrgyz and 15 in Uzbek) were below 0.05 and thus displaying LD (Supplementary Tables 6, 7, 8 and 9). Afer a sequential Bonferroni correction15, only fve pairs were out of LE (Supplementary Table 10). Tese were TH01/D8S1179 and D18S51/D13S317 in the Manchu population, vWA/D21S11 and D2S1338/D19S433 in the Uzbek population and FGA/D13S317 in the Kyrgyz pop- ulation. All pairwise combinations of loci were in LE in the Mongol population. Terefore, of the 105 pairwise LE tests in each population, a maximum of two were out of LE in any population.
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